We want to develop an automated "feature detection" method for use on biological sequences. The method will be an alternative to existing "local similarity" approaches for finding common patterns in multiple sequences. Our method should be both faster and give more complete information about the relationships between regions in the sequences. The method will combine Dr. Myers' new algorithm for the very fast identification of matches to a pattern allowing some number of mismatches, with improvements to an analysis and display method previously developed by the PI and Dr. Ehrenfeucht. We expect that the method will give quantitative, graphical information about repeated patterns (allowing for some differences between instances of the patterns) that can be used to identify important features in the sequences that are typical of known functional domains of DNA and proteins.